my_chemistry.local_dust_to_gas_ratio
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
# timestepping safety factor
safety_factor = 0.01
# let the gas cool at constant density from the starting temperature
# down to a lower temperature to get the species fractions in a
# reasonable state.
cooling_temperature = 100.
data0 = evolve_constant_density(fc,
final_temperature=cooling_temperature,
safety_factor=safety_factor)
# evolve density and temperature according to free-fall collapse
data = evolve_freefall(fc, final_density, safety_factor=safety_factor)
# make a plot of rho/f_H2 vs. T
plots = pyplot.loglog(data["density"],
data["temperature"],
color="black",
label="T$_{gas}$")
if os.environ.get("METAL_COOLING", 0) == "1":
plots.extend(
pyplot.loglog(data["density"],
data["dust_temperature"],
color="black",
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
# timestepping safety factor
safety_factor = 0.01
# let gas cool at constant density
data = evolve_constant_density(fc,
final_time=final_time,
safety_factor=safety_factor)
p1, = pyplot.loglog(data["time"].to("Myr"),
data["temperature"],
color="black",
label="T")
pyplot.xlabel("Time [Myr]")
pyplot.ylabel("T [K]")
data["mu"] = data["temperature"] / \
(data["energy"] * (my_chemistry.Gamma - 1.) *
fc.chemistry_data.temperature_units)
pyplot.twinx()
p2, = pyplot.semilogx(data["time"].to("Myr"),
data["mu"],
def run_grackle(initial_temperature, density, final_time, safety_factor=1e-2):
current_redshift = 0.
tiny_number = 1.0e-20
pygrackle.evolve_constant_density = _new_evolve_constant_density
# Set solver parameters
my_chemistry = chemistry_data()
my_chemistry.three_body_rate = 4
my_chemistry.use_grackle = 1
my_chemistry.with_radiative_cooling = 0
my_chemistry.primordial_chemistry = 2
my_chemistry.metal_cooling = 0
my_chemistry.UVbackground = 0
my_chemistry.self_shielding_method = 0
my_chemistry.H2_self_shielding = 0
grackle_dir = os.path.dirname(
os.path.dirname(
os.path.dirname(os.path.dirname(os.path.abspath(__file__)))))
my_chemistry.grackle_data_file = os.sep.join(
[grackle_dir, "input", "CloudyData_UVB=HM2012.h5"])
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.three_body_rate = 4
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = 1.66053904e-24 # 1u: amu # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = 1.0 # cm
my_chemistry.time_units = 1.0 # s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
tiny_number = 1.0e-20
if my_chemistry.primordial_chemistry > 0:
# these are in mass_density
fc["HI"][:] = 0.76 * fc["density"] / 3.
fc["HII"][:] = 0.76 * fc["density"] / 3.
fc["HeI"][:] = (1 - 0.76) * fc["density"] / 2.
fc["HeII"][:] = (1 - 0.76) * fc["density"] / 2.
fc["HeIII"][:] = tiny_number
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 0.76 * fc["density"] / 3.
fc["H2II"][:] = tiny_number #0.76 * fc["density"] /4.
fc["HM"][:] = tiny_number #0.76 * fc["density"] /4.
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = 0.1 * fc["density"] * \
my_chemistry.SolarMetalFractionByMass
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
# let gas cool at constant density
data = pygrackle.evolve_constant_density(fc,
final_time=final_time,
safety_factor=safety_factor)
return data
def run_grackle(density = 1e10, initial_temperature = 1e3, final_time = 1e5, safety_factor=1e-2):
current_redshift = 0.
tiny_number = 1.0e-20
pygrackle.evolve_constant_density = _new_evolve_constant_density
# Set solver parameters
my_chemistry = chemistry_data()
my_chemistry.three_body_rate = 4
my_chemistry.use_grackle = 1
my_chemistry.with_radiative_cooling = 1
my_chemistry.primordial_chemistry = 2
my_chemistry.metal_cooling = 0
my_chemistry.UVbackground = 0
my_chemistry.self_shielding_method = 0
my_chemistry.H2_self_shielding = 0
my_chemistry.cie_cooling = 0
grackle_dir = "/home/kwoksun2/grackle"
my_chemistry.grackle_data_file = os.sep.join(
[grackle_dir, "input", "CloudyData_UVB=HM2012.h5"])
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.three_body_rate = 4
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = 1.66053904e-24 # 1u: amu # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = 1.0 # cm
my_chemistry.time_units = 1.0 # s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
tiny_number = 1.0e-20
if my_chemistry.primordial_chemistry > 0:
# these are in mass_density
fc["HI"][:] = 0.76 * fc["density"] /3.
fc["HII"][:] = 0.76 * fc["density"] /3.
fc["HeI"][:] = (1 - 0.76) * fc["density"] /2.
fc["HeII"][:] = (1 - 0.76) * fc["density"] /2.
fc["HeIII"][:] = tiny_number
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = 0.76 * fc["density"] /3.
fc["H2II"][:] = tiny_number
fc["HM"][:] = tiny_number
fc["de"][:] = fc["HII"][:] + fc["HeII"][:]/4. + fc["HeIII"][:]/4.*2.0
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = 0.1 * fc["density"] * \
my_chemistry.SolarMetalFractionByMass
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
tic = timeit.default_timer()
# let gas cool at constant density
data = pygrackle.evolve_constant_density(
fc, final_time=final_time,
safety_factor=safety_factor)
toc = timeit.default_timer()
run_time = toc - tic
print("time lapsed", run_time)
# convert grackle language to dengo language
name_map_dict = { 'HI':'H_1',
'HII':'H_2',
'HeI':'He_1',
'HeII':'He_2',
'HeIII':'He_3',
'H2I' : 'H2_1',
'H2II': 'H2_2',
'HM' : 'H_m0',
'de':'de',
'temperature':'T',
'time': 't',
'energy':'ge'}
weight_map_dict = { 'HI':1.00794,
'HII':1.00794,
'HeI':4.002602,
'HeII':4.002602,
'HeIII':4.002602,
'H2II': 2.01588,
'H2I' : 2.01588,
'HM' : 1.00794,
'de':1.00794,
'time': 1.0,
'temperature': 1.0,
'energy': 1.0}
data_grackle = {}
for key in name_map_dict.keys():
key_dengo = name_map_dict[key]
if key_dengo in ["t","T","ge"]:
data_grackle[key_dengo] = data[key].value
else:
data_grackle[key_dengo] = data[key].value / weight_map_dict[key] / u.amu_cgs.value
save_obj(data_grackle, 'grackle_data')
return data_grackle, run_time
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = metal_fraction * fc["density"]
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
# let gas cool at constant density
data = evolve_constant_density(
fc, final_time=final_time,
safety_factor=safety_factor, verbose=False, ignore_time_evolution = True)
eq_temperature[i] = data["temperature"][-1]
eq_density[i] = data["density"][-1]
eq_n_density[i] = data["density"][-1] / (fc.calculate_mean_molecular_weight()[0] * mass_hydrogen_cgs)
eq_pressure[i] = data["pressure"][-1]
file.write("%8.8E %8.8E %8.8E %8.8E\n"%(eq_n_density[i], eq_density[i], eq_temperature[i], eq_pressure[i]))
i = i + 1
file.close()
def cooling_cell(density=12.2,
initial_temperature=2.0E4,
final_time=30.0,
metal_fraction=4.0E-4,
make_plot=False,
save_output=False,
primordial_chemistry=2,
outname=None,
save_H2_fraction=False,
return_result=False,
verbose=False,
H2_converge=None,
*args,
**kwargs):
current_redshift = 0.
# Set solver parameters
my_chemistry = chemistry_data()
my_chemistry.use_grackle = 1
my_chemistry.with_radiative_cooling = 1
my_chemistry.primordial_chemistry = primordial_chemistry
my_chemistry.metal_cooling = 1
my_chemistry.UVbackground = 1
my_chemistry.self_shielding_method = 3
if primordial_chemistry > 1:
my_chemistry.H2_self_shielding = 2
my_chemistry.h2_on_dust = 1
my_chemistry.three_body_rate = 4
grackle_dir = "/home/aemerick/code/grackle-emerick/"
my_chemistry.grackle_data_file = os.sep.join( #['/home/aemerick/code/grackle-emerick/input/CloudyData_UVB=HM2012.h5'])
[grackle_dir, "input", "CloudyData_UVB=HM2012_shielded.h5"])
# set the factors
my_chemistry.LW_factor = kwargs.get("LW_factor", 1.0)
my_chemistry.k27_factor = kwargs.get("k27_factor", 1.0)
#if 'LW_factor' in kwargs.keys():
# my_chemistry.LW_factor = kwargs['LW_factor']
#else:
# my_chemistry.LW_factor = 1.0
#if 'k27_factor' in kwargs.keys():
# my_chemistry.k27_factor = kwargs['k27_factor']
#else:
# my_chemistry.k27_factor = 1.0
# Set units
my_chemistry.comoving_coordinates = 0 # proper units
my_chemistry.a_units = 1.0
my_chemistry.a_value = 1. / (1. + current_redshift) / \
my_chemistry.a_units
my_chemistry.density_units = mass_hydrogen_cgs # rho = 1.0 is 1.67e-24 g
my_chemistry.length_units = cm_per_mpc # 1 Mpc in cm
my_chemistry.time_units = sec_per_Myr # 1 Myr in s
my_chemistry.velocity_units = my_chemistry.a_units * \
(my_chemistry.length_units / my_chemistry.a_value) / \
my_chemistry.time_units
rval = my_chemistry.initialize()
fc = FluidContainer(my_chemistry, 1)
fc["density"][:] = density
if my_chemistry.primordial_chemistry > 0:
fc["HI"][:] = 0.76 * fc["density"]
fc["HII"][:] = tiny_number * fc["density"]
fc["HeI"][:] = (1.0 - 0.76) * fc["density"]
fc["HeII"][:] = tiny_number * fc["density"]
fc["HeIII"][:] = tiny_number * fc["density"]
if my_chemistry.primordial_chemistry > 1:
fc["H2I"][:] = tiny_number * fc["density"]
fc["H2II"][:] = tiny_number * fc["density"]
fc["HM"][:] = tiny_number * fc["density"]
fc["de"][:] = tiny_number * fc["density"]
fc['H2_self_shielding_length'][:] = 1.8E-6
if my_chemistry.primordial_chemistry > 2:
fc["DI"][:] = 2.0 * 3.4e-5 * fc["density"]
fc["DII"][:] = tiny_number * fc["density"]
fc["HDI"][:] = tiny_number * fc["density"]
if my_chemistry.metal_cooling == 1:
fc["metal"][:] = metal_fraction * fc["density"] * \
my_chemistry.SolarMetalFractionByMass
fc["x-velocity"][:] = 0.0
fc["y-velocity"][:] = 0.0
fc["z-velocity"][:] = 0.0
fc["energy"][:] = initial_temperature / \
fc.chemistry_data.temperature_units
fc.calculate_temperature()
fc["energy"][:] *= initial_temperature / fc["temperature"]
# timestepping safety factor
safety_factor = 0.001
# let gas cool at constant density
#if verbose:
print("Beginning Run")
data = evolve_constant_density(fc,
final_time=final_time,
H2_converge=H2_converge,
safety_factor=safety_factor,
verbose=verbose)
#else:
# print "Beginning Run"
# with NoStdStreams():
# data = evolve_constant_density(
# fc, final_time=final_time, H2_converge = 1.0E-6,
# safety_factor=safety_factor)
# print "Ending Run"
if make_plot:
p1, = plt.loglog(data["time"].to("Myr"),
data["temperature"],
color="black",
label="T")
plt.xlabel("Time [Myr]")
plt.ylabel("T [K]")
data["mu"] = data["temperature"] / \
(data["energy"] * (my_chemistry.Gamma - 1.) *
fc.chemistry_data.temperature_units)
plt.twinx()
p2, = plt.semilogx(data["time"].to("Myr"),
data["mu"],
color="red",
label="$\\mu$")
plt.ylabel("$\\mu$")
plt.legend([p1, p2], ["T", "$\\mu$"], fancybox=True, loc="center left")
plt.savefig("cooling_cell.png")
# save data arrays as a yt dataset
if outname is None:
outname = 'cooling_cell_%.2f_%.2f' % (my_chemistry.k27_factor,
my_chemistry.LW_factor)
if save_output:
yt.save_as_dataset({}, outname + '.h5', data)
if my_chemistry.primordial_chemistry > 1:
H2_fraction = (data['H2I'] + data['H2II']) / data['density']
else:
H2_fraction = np.zeros(np.size(data['density']))
if save_H2_fraction:
#np.savetxt(outname + ".dat", [data['time'], H2_fraction])
f = open("all_runs_d_%.2f.dat" % (density), "a")
# f.write("# k27 LW f_H2 T time\n")
f.write("%8.8E %8.8E %8.8E %8.8E %8.8E \n" %
(my_chemistry.k27_factor, my_chemistry.LW_factor,
H2_fraction[-1], data['temperature'][-1], data['time'][-1]))
f.close()
if return_result:
return data
else:
return
